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Conservation and Expression of SNF2 Proteins in Chondrus crispus

The SNF2 families of ATP-dependent helicases are the central catalytic subunits for chromatin remodeling complexes. The most widely studied is the multisubunit SWI/SNF complex, which has been found in plants, yeast, and model organisms. The SWI/SNF core subunit is a member of a smaller subgroup (SNF2 subfamiy) within the larger SNF2 super-family. In a recent study of two red algae, members of most SNF2 helicase sub-families were found to be present, although it appeared unlikely that the multi-subunit SWI/SNF remodeling complexes were formed based on available gene expression data. The core SWI/SNF complex is made up of four major proteins; Swi2/Snf2, Swi3, Swp73, and Snf5. The complete genome of another red algae, Chondrus crispus, recently was sequenced and examined to see whether the major SWI/SNF components were conserved. Using known protein sequences obtained from model organisms, SWI/SNF complex protein sequences were searched using the BLAST tool found on the NCBI website. Paralogs from the broader SNF2 ATPase super-family were determined in Chondrus and carefully identified to subfamily using maximum-likelihood phylogenetic analyses. The combined bioinformatics analyses revealed that Chondrus contains sequences from each major group of the SNF2 protein complexes. Expression date revealed that three of the four core components of the SWI/SNF complex are expressed. Even with the lack of expression from the swi73 gene the SWI/SNF and INO80 complex were found to have correlating expression data in 15 out of 18 replicates. This data suggest that there could be comparable chromatin remodeling complexes in red algae however, they may not include the same core proteins.